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# Sys.getenv("RSTUDIO_PANDOC")
# Sys.setenv(RSTUDIO_PANDOC= "/c/Program Files/RStudio/bin/pandoc/")
# remove.packages('vctrs')
# install.packages('vctrs')
# packageVersion('vctrs')
library(namespace)
library(corrplot)

corrplot 0.84 loaded

require("survival")

Loading required package: survival

require(statar)

Loading required package: statar

library(statar)
library(ggplot2)
library(ggpubr)
library(readxl)
library(tidyr)

pan_immune_matrix=readxl::read_xlsx('../data/1-s2.0-S1074761318301213-mmc2.xlsx')

New names:
* Eosinophils -> Eosinophils...41
* Neutrophils -> Neutrophils...48
* Neutrophils -> Neutrophils...60
* Eosinophils -> Eosinophils...61

pan_immune_matrix

pan_immune_matrix_prep= pan_immune_matrix[,-c(1, 3, 4)]
pan_immune_matrix_prep=data.frame(pan_immune_matrix_prep[,1], apply(pan_immune_matrix_prep[,-1], 2, as.numeric))

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immune_cells_by_cancerType=aggregate(.~TCGA.Study , pan_immune_matrix_prep,
                                     function(x) median(x, na.rm=T),  na.action = NULL)

rownames(immune_cells_by_cancerType)=immune_cells_by_cancerType$TCGA.Study
immune_cells_by_cancerType=rbind(immune_cells_by_cancerType, 
                                 NSCLC=c('NSCLC',colMeans(immune_cells_by_cancerType[
                                   immune_cells_by_cancerType$TCGA.Study=='LUSC'|
                                     immune_cells_by_cancerType$TCGA.Study=='LUAD',-(1)])))
immune_cells_by_cancerType=data.frame(apply(immune_cells_by_cancerType[,-1], 2, as.numeric),
                                      row.names = rownames(immune_cells_by_cancerType))

colnames(immune_cells_by_cancerType)

 [1] "Leukocyte.Fraction"                     
 [2] "Stromal.Fraction"                       
 [3] "Intratumor.Heterogeneity"               
 [4] "TIL.Regional.Fraction"                  
 [5] "Proliferation"                          
 [6] "Wound.Healing"                          
 [7] "Macrophage.Regulation"                  
 [8] "Lymphocyte.Infiltration.Signature.Score"
 [9] "IFN.gamma.Response"                     
[10] "TGF.beta.Response"                      
[11] "SNV.Neoantigens"                        
[12] "Indel.Neoantigens"                      
[13] "Silent.Mutation.Rate"                   
[14] "Nonsilent.Mutation.Rate"                
[15] "Number.of.Segments"                     
[16] "Fraction.Altered"                       
[17] "Aneuploidy.Score"                       
[18] "Homologous.Recombination.Defects"       
[19] "BCR.Evenness"                           
[20] "BCR.Shannon"                            
[21] "BCR.Richness"                           
[22] "TCR.Shannon"                            
[23] "TCR.Richness"                           
[24] "TCR.Evenness"                           
[25] "CTA.Score"                              
[26] "Th1.Cells"                              
[27] "Th2.Cells"                              
[28] "Th17.Cells"                             
[29] "OS"                                     
[30] "OS.Time"                                
[31] "PFI"                                    
[32] "PFI.Time"                               
[33] "B.Cells.Memory"                         
[34] "B.Cells.Naive"                          
[35] "Dendritic.Cells.Activated"              
[36] "Dendritic.Cells.Resting"                
[37] "Eosinophils...41"                       
[38] "Macrophages.M0"                         
[39] "Macrophages.M1"                         
[40] "Macrophages.M2"                         
[41] "Mast.Cells.Activated"                   
[42] "Mast.Cells.Resting"                     
[43] "Monocytes"                              
[44] "Neutrophils...48"                       
[45] "NK.Cells.Activated"                     
[46] "NK.Cells.Resting"                       
[47] "Plasma.Cells"                           
[48] "T.Cells.CD4.Memory.Activated"           
[49] "T.Cells.CD4.Memory.Resting"             
[50] "T.Cells.CD4.Naive"                      
[51] "T.Cells.CD8"                            
[52] "T.Cells.Follicular.Helper"              
[53] "T.Cells.gamma.delta"                    
[54] "T.Cells.Regulatory.Tregs"               
[55] "Lymphocytes"                            
[56] "Neutrophils...60"                       
[57] "Eosinophils...61"                       
[58] "Mast.Cells"                             
[59] "Dendritic.Cells"                        
[60] "Macrophages"                            

Leukocyte.Fraction

Stromal.Fraction

Intratumor.Heterogeneity

TIL.Regional.Fraction

Proliferation

Wound.Healing

Macrophage.Regulation

Lymphocyte.Infiltration.Signature.Score

IFN.gamma.Response

TGF.beta.Response

SNV.Neoantigens

Indel.Neoantigens

Silent.Mutation.Rate

Nonsilent.Mutation.Rate

Number.of.Segments

Fraction.Altered

Aneuploidy.Score

Homologous.Recombination.Defects

BCR.Evenness

BCR.Shannon

BCR.Richness

TCR.Shannon

TCR.Richness

TCR.Evenness

CTA.Score

Th1.Cells

Th2.Cells

Th17.Cells

OS

OS.Time

PFI

PFI.Time

B.Cells.Memory

B.Cells.Naive

Dendritic.Cells.Activated

Dendritic.Cells.Resting

Eosinophils...41

Macrophages.M0

Macrophages.M1

Macrophages.M2

Mast.Cells.Activated

Mast.Cells.Resting

Monocytes

Neutrophils...48

NK.Cells.Activated

NK.Cells.Resting

Plasma.Cells

T.Cells.CD4.Memory.Activated

T.Cells.CD4.Memory.Resting

T.Cells.CD4.Naive

T.Cells.CD8

T.Cells.Follicular.Helper

T.Cells.gamma.delta

T.Cells.Regulatory.Tregs

Lymphocytes

Neutrophils...60

Eosinophils...61

Mast.Cells

Dendritic.Cells

Macrophages

non_immune_signature=c("Proliferation", "Wound.Healing", "Intratumor.Heterogeneity",
                        "SNV.Neoantigens",
                       "Indel.Neoantigens","Silent.Mutation.Rate","Nonsilent.Mutation.Rate",
                       "Number.of.Segments","Fraction.Altered",
                       "Aneuploidy.Score",
                       "Homologous.Recombination.Defects")

immune_signature=c("Macrophage.Regulation","Lymphocyte.Infiltration.Signature.Score",
                   "IFN.gamma.Response","TGF.beta.Response", "IFN.gamma.Response",
                   "BCR.Evenness", "BCR.Shannon", "BCR.Richness","TCR.Shannon",
                       "TCR.Richness","TCR.Evenness", "TGF.beta.Response")

to_remove=c("OS", "OS.Time", "PFI", "PFI.Time", "Neutrophils...60", "Eosinophils...61")
immune_cells_by_cancerType=immune_cells_by_cancerType[,!(colnames(immune_cells_by_cancerType) %in% to_remove)]
colnames(immune_cells_by_cancerType)

 [1] "Leukocyte.Fraction"                     
 [2] "Stromal.Fraction"                       
 [3] "Intratumor.Heterogeneity"               
 [4] "TIL.Regional.Fraction"                  
 [5] "Proliferation"                          
 [6] "Wound.Healing"                          
 [7] "Macrophage.Regulation"                  
 [8] "Lymphocyte.Infiltration.Signature.Score"
 [9] "IFN.gamma.Response"                     
[10] "TGF.beta.Response"                      
[11] "SNV.Neoantigens"                        
[12] "Indel.Neoantigens"                      
[13] "Silent.Mutation.Rate"                   
[14] "Nonsilent.Mutation.Rate"                
[15] "Number.of.Segments"                     
[16] "Fraction.Altered"                       
[17] "Aneuploidy.Score"                       
[18] "Homologous.Recombination.Defects"       
[19] "BCR.Evenness"                           
[20] "BCR.Shannon"                            
[21] "BCR.Richness"                           
[22] "TCR.Shannon"                            
[23] "TCR.Richness"                           
[24] "TCR.Evenness"                           
[25] "CTA.Score"                              
[26] "Th1.Cells"                              
[27] "Th2.Cells"                              
[28] "Th17.Cells"                             
[29] "B.Cells.Memory"                         
[30] "B.Cells.Naive"                          
[31] "Dendritic.Cells.Activated"              
[32] "Dendritic.Cells.Resting"                
[33] "Eosinophils...41"                       
[34] "Macrophages.M0"                         
[35] "Macrophages.M1"                         
[36] "Macrophages.M2"                         
[37] "Mast.Cells.Activated"                   
[38] "Mast.Cells.Resting"                     
[39] "Monocytes"                              
[40] "Neutrophils...48"                       
[41] "NK.Cells.Activated"                     
[42] "NK.Cells.Resting"                       
[43] "Plasma.Cells"                           
[44] "T.Cells.CD4.Memory.Activated"           
[45] "T.Cells.CD4.Memory.Resting"             
[46] "T.Cells.CD4.Naive"                      
[47] "T.Cells.CD8"                            
[48] "T.Cells.Follicular.Helper"              
[49] "T.Cells.gamma.delta"                    
[50] "T.Cells.Regulatory.Tregs"               
[51] "Lymphocytes"                            
[52] "Mast.Cells"                             
[53] "Dendritic.Cells"                        
[54] "Macrophages"                            

Leukocyte.Fraction

Stromal.Fraction

Intratumor.Heterogeneity

TIL.Regional.Fraction

Proliferation

Wound.Healing

Macrophage.Regulation

Lymphocyte.Infiltration.Signature.Score

IFN.gamma.Response

TGF.beta.Response

SNV.Neoantigens

Indel.Neoantigens

Silent.Mutation.Rate

Nonsilent.Mutation.Rate

Number.of.Segments

Fraction.Altered

Aneuploidy.Score

Homologous.Recombination.Defects

BCR.Evenness

BCR.Shannon

BCR.Richness

TCR.Shannon

TCR.Richness

TCR.Evenness

CTA.Score

Th1.Cells

Th2.Cells

Th17.Cells

B.Cells.Memory

B.Cells.Naive

Dendritic.Cells.Activated

Dendritic.Cells.Resting

Eosinophils...41

Macrophages.M0

Macrophages.M1

Macrophages.M2

Mast.Cells.Activated

Mast.Cells.Resting

Monocytes

Neutrophils...48

NK.Cells.Activated

NK.Cells.Resting

Plasma.Cells

T.Cells.CD4.Memory.Activated

T.Cells.CD4.Memory.Resting

T.Cells.CD4.Naive

T.Cells.CD8

T.Cells.Follicular.Helper

T.Cells.gamma.delta

T.Cells.Regulatory.Tregs

Lymphocytes

Mast.Cells

Dendritic.Cells

Macrophages

# Immune_matrix_TCGA= t(immune_cells_by_cancerType)

Immune_Cell_abundance=immune_cells_by_cancerType[,!(colnames(immune_cells_by_cancerType) %in% c(non_immune_signature, immune_signature))]
Immune_Signature_abundance=immune_cells_by_cancerType[,colnames(immune_cells_by_cancerType) %in%  immune_signature]
nonImmune_Signature_abundance=immune_cells_by_cancerType[,colnames(immune_cells_by_cancerType) %in%  non_immune_signature]

colnames(Immune_Cell_abundance)[grep('Neutrophils',colnames(Immune_Cell_abundance))]='Neutrophils'

immune_factor= read.csv("../data/immune_factors_response_joo_v2.csv", row.names = 1)

f1=18/(18+31); f2=1-f1
immune_factor$COAD= sapply(seq(1:nrow(immune_factor)), function (x) 
  (as.numeric(immune_factor[x,'COAD_MSI'])* f1 + as.numeric(immune_factor[x,'COAD_MSS'])* f2))
immune_factor$NSCLC= sapply(seq(1:nrow(immune_factor)), function (x) 
  (immune_factor[x,'LUAD']* 0.5 + immune_factor[x,'LUAD']* 0.5))

immune_factor= data.frame(t(immune_factor))
# mapping=match(rownames(immune_factor), rownames(Immune_Cell_abundance))
# immune_factor$Lymphocytes=(Immune_Cell_abundance$Lymphocytes)[mapping]
# immune_factor$NTL=(Immune_Cell_abundance$Neutrophils/Immune_Cell_abundance$Lymphocytes)[mapping]

colnames(immune_factor)[grep('CPS',colnames(immune_factor))]=
  'PDL1 (combined positive score)'

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